Find PDB structures and Computed Structure Models (CSM) by combining queries from tools in this suite: Attribute Search, Sequence Similarity, Sequence Motif, 3D Similarity, and 3D Motif with 'AND' logic.
Structure of full-length LexA bound to a RecA filament
ELECTRON MICROSCOPY
Starting Model(s)
Initial Refinement Model(s)
Type
Source
Accession Code
Details
in silico model
AlphaFold
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
f_dihedral_angle_d
12.762
f_angle_d
0.655
f_chiral_restr
0.045
f_plane_restr
0.006
f_bond_d
0.005
Sample
SOS Signal Complex consisting of RecA, ssDNA, and LexA
Sample Components
RecA* activated filament
LexA Dimer
Specimen Preparation
Sample Aggregation State
FILAMENT
Vitrification Instrument
FEI VITROBOT MARK IV
Cryogen Name
ETHANE
Sample Vitrification Details
Blotting time of 7.0 s; 0.0 blot force
3D Reconstruction
Reconstruction Method
HELICAL
Number of Particles
233920
Reported Resolution (Å)
2.93
Resolution Method
FSC 0.143 CUT-OFF
Other Details
Refinement Type
Symmetry Type
HELICAL
Axial Symmetry
C1
Axial Rise
16.23
Angular Rotation
59.2
Axial Symmetry
C1
Axial Rise
16.23
Angular Rotation
59.2
Axial Symmetry
C1
Axial Rise
16.23
Angular Rotation
59.2
Axial Symmetry
C1
Axial Rise
16.23
Angular Rotation
59.2
Map-Model Fitting and Refinement
Id
1
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
Fitting Procedure
Details
Data Acquisition
Detector Type
GATAN K3 (6k x 4k)
Electron Dose (electrons/Å**2)
46.2
Imaging Experiment
1
Date of Experiment
Temperature (Kelvin)
Microscope Model
FEI TITAN KRIOS
Minimum Defocus (nm)
500
Maximum Defocus (nm)
2000
Minimum Tilt Angle (degrees)
Maximum Tilt Angle (degrees)
Nominal CS
2.7
Imaging Mode
BRIGHT FIELD
Specimen Holder Model
FEI TITAN KRIOS AUTOGRID HOLDER
Nominal Magnification
64000
Calibrated Magnification
Source
FIELD EMISSION GUN
Acceleration Voltage (kV)
300
Imaging Details
Preliminary grid screening was done manually
EM Software
Task
Software Package
Version
PARTICLE SELECTION
cryoSPARC
4.0.3
IMAGE ACQUISITION
EPU
CTF CORRECTION
cryoSPARC
4.0.3
MODEL FITTING
UCSF ChimeraX
1.3
MODEL REFINEMENT
PHENIX
1.20.1
MODEL REFINEMENT
ISOLDE
1.4
CLASSIFICATION
cryoSPARC
4.0.3
RECONSTRUCTION
cryoSPARC
4.0.3
Image Processing
CTF Correction Type
CTF Correction Details
Number of Particles Selected
Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION
3423408
cryoSPARC automated Filament Tracer using filament diameter of 100A, 17A separation between segments. Minimum and maximum filament diameters of 90A, 150A respectively.
Inspect Picks to filter particles with high curvature or sinuosity
Local power > 567.940
Local power < 5711.103
Curvature (1/A) < 0.005970
Sinuosity < 1.393924
Low pass filtered particles near micrograph edge.